The earliest European reference to the mosque appears in a description from November 1505 when the commander of a Portuguese expedition anchored in Colombo bay.

In 1520 following an attack on the Portuguese trading post, established earlier by Lopo de Brito, the Captain of Portuguese Ceylon, the King Bhuvanaikabahu of Kotte burnt the town (Colombo) along with two large mosques.

In the 1820s, the mosque was redesigned and rebuilt by Malay architect, Muhammad Balangkaya, the son of a Malay noble of the Royal House of Gowa (present-day Sulawesi, Indonesia),[1][2] who was exiled to Ceylon in 1790 by the Dutch.

[3] In 1826 the British Governor of Ceylon, Edward Barnes, visited the mosque and commended the architect on the excellence of his work.

The mosque contains the shrine of the Malay saint, Bahu-Uddeen Tuan Bagoos Balankaya.